CompaRNA - on-line benchmarks of RNA structure prediction methods

CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Table of contents:

Overview

Performance Plots

Performance of TurboFold(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of CRWrnafold - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for TurboFold(20) & CRWrnafold [.zip] - may take several seconds...

Overview

Metric	TurboFold(20)		CRWrnafold
MCC	0.683	>	0.668
Average MCC ± 95% Confidence Intervals	0.681 ± 0.195	<	0.692 ± 0.219
Sensitivity	0.646	<	0.683
Positive Predictive Value	0.731	>	0.663
Total TP	106	<	112
Total TN	12229	>	12205
Total FP	54	<	83
Total FP CONTRA	11	<	18
Total FP INCONS	28	<	39
Total FP COMP	15	<	26
Total FN	58	>	52
P-value	0.0

Performance plots

Comparison of performance of TurboFold(20) and CRWrnafold. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for TurboFold(20) and CRWrnafold).
Comparison of average Matthews Correlation Coefficients (MCCs) for TurboFold(20) and CRWrnafold. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for TurboFold(20) and CRWrnafold).

Performance of TurboFold(20) - scored higher in this pairwise comparison

1. Total counts & total scores for TurboFold(20)

Total Base Pair Counts
Total TP	106
Total TN	12229
Total FP	54
Total FP CONTRA	11
Total FP INCONS	28
Total FP COMP	15
Total FN	58

Total Scores
MCC	0.683
Average MCC ± 95% Confidence Intervals	0.681 ± 0.195
Sensitivity	0.646
Positive Predictive Value	0.731
Nr of predictions	7

2. Individual counts for TurboFold(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3SD1_A	THF links to Rfam database...	0.71	0.69	0.74	20	1506	7	2	5	0	9
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.84	0.89	31	2728	6	0	4	2	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.21	5	4492	28	6	13	9	15
4AOB_A	SAM links to Rfam database...	0.67	0.59	0.77	17	1415	6	2	3	1	12
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6

Performance of CRWrnafold - scored lower in this pairwise comparison

1. Total counts & total scores for CRWrnafold

Total Base Pair Counts
Total TP	112
Total TN	12205
Total FP	83
Total FP CONTRA	18
Total FP INCONS	39
Total FP COMP	26
Total FN	52

Total Scores
MCC	0.668
Average MCC ± 95% Confidence Intervals	0.692 ± 0.219
Sensitivity	0.683
Positive Predictive Value	0.663
Nr of predictions	7

2. Individual counts for CRWrnafold [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3SD1_A	THF links to Rfam database...	0.63	0.66	0.61	19	1502	12	6	6	0	10
4A1C_3	5S_rRNA links to Rfam database...	0.85	0.84	0.86	31	2727	7	0	5	2	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	44	8	20	16	15
4AOB_A	SAM links to Rfam database...	0.71	0.69	0.74	20	1410	8	4	3	1	9
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	2	0	0	2	4

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.